Genetic differentiation of relictual populations of Alsophila spinulosa in southern China inferred from cpDNA trnL–F noncoding sequences

Geographic isolation and environmental heterogeneity contribute to genetic differentiation in Cephalotaxus oliveri

Evaluating the contributions of geographic distance and environmental heterogeneity to the genetic divergence can inform the demographic history and responses to environmental change of natural populations. The isolation-by-distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation-by-environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations. Here, we sampled and genotyped 330 individuals from 18 natural populations of Cephalotaxus oliveri throughout the species' distribution. Twenty-eight EST-SSR markers were applied to analyze population genetics, for the investigation of the driving factors that shaped spatial structure. In addition, we identified the outlier loci under positive selection and tested their association with environmental factors. The results showed a moderate genetic diversity in C. oliveri and high genetic differentiation among populations. Population structure analyses indicated that 18 populations were clustered into two major groups. We observed that the genetic diversity of central populations decreased and the genetic differentiation increased towards the marginal populations. Additionally, the signatures of IBD and IBE were detected in C. oliveri, and IBE provided a better contribution to genetic differentiation. Six outlier loci under positive selection were demonstrated to be closely correlated with environmental variables, among which bio8 was associated with the greatest number of loci. Genetic evidence suggests the consistency of the central-marginal hypothesis (CMH) for C. oliveri. Furthermore, our results suggest that temperature-related variables played an important role in shaping genetic differentiation.

Moso Bamboo Invasion Reshapes Community Structure of Denitrifying Bacteria in Rhizosphere of Alsophila spinulosa

The uncontrolled invasion of moso bamboo (Phyllostachys pubescens) dramatically alters soil nitrogen cycling and destroys the natural habitat of Alsophila spinulosa. Nevertheless, no clear evidence points out the role of denitrifying bacteria in the invasion of bamboo into the habitat of A. spinulosa. In the present study, we found that low (importance value 0.0008), moderate (0.6551), and high (0.9326) bamboo invasions dramatically altered the underground root biomass of both P. pubescens and A. spinulosa. The root biomass of A. spinulosa was maximal at moderate invasion, indicating that intermediate disturbance might contribute to the growth and survival of the colonized plant. Successful bamboo invasion significantly increased rhizospheric soil available nitrogen content of A. spinulosa, coupled with elevated denitrifying bacterial abundance and diversity. Shewanella, Chitinophaga, and Achromobacter were the primary genera in the three invasions, whereas high bamboo invasion harbored more denitrifying bacteria and higher abundance than moderate and low invasions. Further correlation analysis found that most soil denitrifying bacteria were positively correlated with soil organic matter and available nitrogen but negatively correlated with pH and water content. In addition, our findings illustrated that two denitrifying bacteria, Chitinophaga and Sorangium, might be essential indicators for evaluating the effects of bamboo invasion on the growth of A. spinulosa. Collectively, this study found that moso bamboo invasion could change the nitrogen cycling of colonized habitats through alterations of denitrifying bacteria and provided valuable perspectives for profound recognizing the invasive impacts and mechanisms of bamboo expansion.

Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.

High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha

Why invasive species can rapidly adapt to novel environments is a puzzling question known as the genetic paradox of invasive species. This paradox is explainable in terms of transposable elements (TEs) activity, which are theorized to be powerful mutational forces to create genetic variation. Mikania micrantha, a noxious invasive weed, in this sense provides an excellent opportunity to test the explanation. The genetic and epigenetic variation of 21 invasive populations of M. micrantha in southern China have been examined by using transposon display (TD) and transposon methylation display (TMD) techniques to survey 12 TE superfamilies. Our results showed that M. micrantha populations maintained an almost equally high level of TE-based genetic and epigenetic variation and they have been differentiated into subpopulations genetically and epigenetically. A similar positive spatial genetic and epigenetic structure pattern was observed within 300 m. Six and seven TE superfamilies presented significant genetic and epigenetic isolation by distance (IBD) pattern. In total, 59 genetic and 86 epigenetic adaptive TE loci were identified. Of them, 51 genetic and 44 epigenetic loci were found to correlate with 25 environmental variables (including precipitation, temperature, vegetation coverage, and soil metals). Twenty-five transposon-inserted genes were sequenced and homology-based annotated, which are found to be involved in a variety of molecular and cellular functions. Our research consolidates the importance of TE-associated genetic and epigenetic variation in the rapid adaptation and invasion of M. micrantha.

Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha

A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.

Characterization and Application of EST-SSR Markers Developed From the Transcriptome of Amentotaxus argotaenia (Taxaceae), a Relict Vulnerable Conifer

Amentotaxus argotaenia (Taxaceae) is a vulnerable coniferous species with preference for shade and moist environment. Accurate estimation of genetic variation is crucial for its conservation, especially in the context of global warming. In this study, we acquired a transcriptome from A. argotaenia leaves using Illumina sequencing and de novo assembled 62,896 unigenes, of which 5510 EST-SSRs were detected. Twenty-two polymorphic EST-SSRs were successfully developed and further used to investigate genetic variation, linkage disequilibrium, and bottleneck signatures of A. argotaenia. The results showed that A. argotaenia had moderate genetic variation and high genetic differentiation, which may provide raw material to protect against climatic changes and accelerate local adaptation, respectively. No bottlenecks were found to occur in A. argotaenia. Our study not only showed that these EST markers are very effective in population genetic analysis but also lay a solid foundation for further investigating adaptive evolution and conservation strategies of A. argotaenia.

Chloroplast population genetics reveals low levels of genetic variation and conformation to the central-marginal hypothesis in Taxus wallichiana var. mairei, an endangered conifer endemic to China

The central-marginal hypothesis predicts that geographically peripheral populations should exhibit reduced genetic diversity and increased genetic differentiation than central populations due to smaller effective population size and stronger geographical isolation. We evaluated these predictions in the endangered conifer Taxus wallichiana var. mairei. Eight plastid simple sequence repeats (cpSSRs) were used to investigate plastid genetic variation in 22 populations of Taxus wallichiana var. mairei, encompassing nearly its entire distribution range. Low levels of plastid genetic variation and differentiation were detected in the populations, and the findings were attributed to low mutation rates, small population sizes, habitat fragmentation and isolation, and effective pollen or seed dispersal. Hunan and Hubei were identified as major refugia based on the number of private haplotypes and species distribution modeling. Trends in plastid genetic diversity and genetic differentiation from central to peripheral populations supported the predictions of the central-marginal hypothesis. In scenarios wherein the future climate becomes warmer, we predict that some peripheral populations will disappear and southern and southeastern regions will become significantly less habitable. Factors that include the levels of precipitation during the driest month, annual precipitation level, and annual temperature range will be decisive in shaping the future distribution of these populations. This study provides a theoretical basis for the conservation of T. wallichiana var. mairei.

Conservation of genetic diversity hotspots of the high-valued relic yellowhorn (Xanthoceras sorbifolium) considering climate change predictions

Genetic structure and major climate factors may contribute to the distribution of genetic diversity of a highly valued oil tree species Xanthoceras sorbifolium (yellowhorn). Long-term over utilization along with climate change is affecting the viability of yellowhorn wild populations. To preserve the species known and unknown valuable gene pools, the identification of genetic diversity "hotspots" is a prerequisite for their consideration as in situ conservation high priority. Chloroplast DNA (cpDNA) diversity was high among 38 natural populations (H d = 0.717, K = 4.616, Tajmas' D = -0.22) and characterized by high genetic divergence (F ST = 0.765) and relatively low gene flow (N m = 0.03), indicating populations isolation reflecting the species' habitat fragmentation and inbreeding depression. Six out of the studied 38 populations are defined as genetic diversity "hotspots." The number and geographic direction of cpDNA mutation steps supported the species southwest to northeast migration history. Climatic factors such as extreme minimum temperature over 30 years indicated that the identified genetic "hotspots" are expected to experience 5°C temperature increase in next following 50 years. The results identified vulnerable genetic diversity "hotspots" and provided fundamental information for the species' future conservation and breeding activities under the anticipated climate change. More specifically, the role of breeding as a component of a gene resource management strategy aimed at fulfilling both utilization and conservation goals.

Methylation data from Pseudotaxus chienii obtained using methylation-dependent restriction-site associated DNA sequencing

Pseudotaxus chienii is an endangered coniferous plant that is endemic to China. Because P. chienii is sessile and has a long life cycle, its options for responding to drastic or rapid changes in climate are limited. To survive locally, P. chienii must be able to adapt, and the species shows variations in leaf size along an environmental gradient from east to west. It is important to determine whether this phenotypic variation is driven by DNA methylation. Therefore, we performed a preliminarily survey using methylation-dependent restriction-site associated DNA sequencing (MethylRAD) to investigate the methylation status of three P. chienii individuals from heterogeneous ecological niches. In total, 372,611 CCGG tags and 726,332 CCHGG tags were obtained. The rate of high quality methylation tags for a specific site in the genome varied from 42.31% (Gxdms3-4) to 50.01% (Jxbj3-4) and 50.18% (Zjdxg3-6). The level of CCHGG methylation (16.63%) was higher than that of CCGG (13.60%), which may be why P. chienii has low levels of phenotypic variation. The methylation data can be accessed using the Sequence Read Archive (SRA) database (SRP128155).

Development and characterization of 23 polymorphic microsatellite loci for Amentotaxus argotaenia (Taxaceae), a relict vulnerable species

PREMISE OF THE STUDY

New microsatellite markers were developed for the vulnerable conifer species Amentotaxus argotaenia (Taxaceae) to investigate population genetic variation and the effects of environmental heterogeneity on genetic structure.

METHODS AND RESULTS

A total of 27 microsatellite loci were developed from A. argotaenia through a Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol, of which 23 were polymorphic. These markers yielded 1-13 alleles and 1.0-7.9 effective alleles per locus; levels of observed and expected heterozygosity varied from 0.000-1.000 and 0.000-0.873, respectively. In total, 18 of the markers were transferable to the related species A. yunnanensis.

CONCLUSIONS

These polymorphic markers are a valuable genetic resource for investigating population genetic variation and the potential for local adaptation in A. argotaenia.

Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.

Experimental evidence for an intraspecific Janzen-Connell effect mediated by soil biota

The negative effect of soil pathogens on seedling survival varies considerably among conspecific individuals, but the underlying mechanisms are largely unknown. For variation between heterospecifics, a common explanation is the Janzen-Connell effect: negative density dependence in survival due to specialized pathogens aggregating on common hosts. We test whether an intraspecific Janzen-Connell effect exists, i.e., whether the survival chances of one population's seedlings surrounded by a different conspecific population increase with genetic difference, spatial distance, and trait dissimilarity between them. In a shade-house experiment, we grew seedlings of five populations of each of two subtropical tree species (Castanopsis fissa and Canarium album) for which we measured genetic distance using intersimple sequence repeat (ISSR) analysis and eight common traits/characters, and we treated them with soil material or soil biota filtrate collected from different populations. We found that the relative survival rate increased with increasing dissimilarity measured by spatial distance, genetic distance, and trait differences between the seedling and the population around which the soil was collected. This effect disappeared after soil sterilization. Our results provide evidence that genetic variation, trait similarity, and spatial distance can explain intraspecific variation in plant-soil biotic interactions and suggest that limiting similarity also occurs at the intraspecific level.

Molecular data and ecological niche modeling reveal population dynamics of widespread shrub Forsythia suspensa (Oleaceae) in China's warm-temperate zone in response to climate change during the Pleistocene

Background

Despite its high number of endemic deciduous broad-leaved species in China’s warm-temperate zone, far less attention has been paid to phylogeographic studies in this region. In this work, the phylogeographic history of Forsythia suspensa endemic to China’s warm-temperate zone was investigated to explore the effect of climate change during the Pleistocene on the distribution of this deciduous broad-leaved species in China.

Results

The cpDNA data revealed seven phylogeographical groups corresponding to geographical regions. By contrast, the nrDNA data supported the samples clustered into three groups, which was inconsistent with separate geographical regions supported by cpDNA data. Ecological niche modeling showed that the climatically suitable area during the cold period was larger than that during the warm period.

Conclusions

Both molecular data and ecological niche modeling indicated that F. suspensa expanded to nearby low-elevation plains in the glacial periods, and retreated to mountaintops during interglacial warmer stages. This study thus supported that F. suspensa persisted in situ during the glacial of the Pleistocene with enlarged distribution area, contrary to the hypothesis of long distance southward migration or large-scale range contraction.

Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae): effects of reproductive strategy

Background

Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation.

Methodology/Principal Findings

Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG) in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations.

Conclusions/Significance

Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

Low but structured chloroplast diversity in Atherosperma moschatum (Atherospermataceae) suggests bottlenecks in response to the Pleistocene glacials

BACKGROUND AND AIMS

The cool temperate rainforests of Australia were much reduced in range during the cold and dry glacial periods, although genetic evidence indicates that two key rainforest species, Nothofagus cunninghamii and Tasmannia lanceolata, survived within multiple locations and underwent only local range expansions at the end of the Last Glacial. To better understand the glacial response of a co-occurring but wind-dispersed and less cold-tolerant rainforest tree species, Atherosperma moschatum, a chloroplast phylogeographic study was undertaken.

METHODS

A total of 3294 bp of chloroplast DNA sequence was obtained for 155 samples collected from across the species' range.

KEY RESULTS

The distribution of six haplotypes observed in A. moschatum was geographically structured with an inferred ancestral haplotype restricted to Tasmania, while three non-overlapping and endemic haplotypes were found on the mainland of south-eastern Australia. Last glacial refugia for A. moschatum are likely to have occurred in at least one location in western Tasmania and in Victoria and within at least two locations in the Great Dividing Range of New South Wales. Nucleotide diversity of A. moschatum was lower (π = 0·00021) than either N. cunninghamii (0·00101) or T. lanceolata (0·00073), and was amongst the lowest recorded for any tree species.

CONCLUSIONS

This study provides evidence for past bottlenecks having impacted the chloroplast diversity of A. moschatum as a result of the species narrower climatic niche during glacials. This hypothesis is supported by the star-like haplotype network and similar estimated rates of chloroplast DNA substitution for A. moschatum and the two more cold tolerant and co-occurring species that have higher chloroplast diversity, N. cunninghamii and T. lanceolata.

Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora

The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-)temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences of the main phylogeographic findings in light of palaeo-environmental evidence, emphasize notable gaps in our knowledge, and outline future research prospects for disentangling the evolution and biogeographic history of the region's extremely diverse temperate flora.

Strong phylogeographic pattern of cpDNA variation reveals multiple glacial refugia for Saruma henryi Oliv. (Aristolochiaceae), an endangered herb endemic to China

Saruma henryi Oliv. (Aristolochiaceae) is an endangered herb endemic to China. In this study, chloroplast microsatellites (cpSSRs) and sequences of the atpB-rbcL intergenic spacers were employed to reveal its genetic diversity and phylogeographic patterns. We detected high within-species genetic diversity (H(T)=0.939 for cpSSR; H(T)=0.862 for atpB-rbcL) and pronounced among-population genetic differentiation (H(S)=0.182, G(ST)=0.811, R(ST)=0.9, F(ST)=0.93 for cpSSR; H(S)=0.238, G(ST)=0.724, N(ST)=0.758, F(ST)=0.79 for atpB-rbcL) with a strong phylogeographic pattern (R(ST)>G(ST), P<0.01 for cpSSR; N(ST)>G(ST), U=0.25 for atpB-rbcL). Eleven haplotypes were distinguished by cpSSRs and atpB-rbcL intergenic spacers, respectively. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggested the existence of multiple localized glacial refugia in Mts. Qinling, eastern Mts. Bashan and the southeastern edge of Yunnan-Guizhou Plateau. Nested clade analysis (NCA) and population genetic analyses supported the limited gene flow (caused by low dispersal capacity and complex topography of its habitats) as the major factor responsible for the strong population differentiation and phylogeographic pattern. Past fragmentation and allopatric fragmentation were inferred as important processes responsible for the modern phylogeograhpic pattern. In addition, contiguous range expansions occurred in western Mts. Qinling and eastern Mts. Bashan.

Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fernAsplenium hookerianum

In the Southern Hemisphere there has been little phylogeographical investigation of forest refugia sites during the last glacial. Hooker's spleenwort, Asplenium hookerianum, is a fern that is found throughout New Zealand. It is strongly associated with forest and is a proxy for the survival of woody vegetation during the last glacial maximum. DNA sequence data from the chloroplast trnL-trnF locus were obtained from 242 samples, including c. 10 individuals from each of 21 focal populations. Most populations contained multiple, and in many cases unique, haplotypes, including those neighbouring formerly glaciated areas, while the predominant inference from nested clade analysis was restricted gene flow with isolation by distance. These results suggest that A. hookerianum survived the last glacial maximum in widespread populations of sufficient size to retain the observed phylogeography, and therefore that the sheltering woody vegetation must have been similarly abundant. This is consistent with palynological interpretations for the survival in New Zealand of thermophilous forest species at considerably smaller distances from the ice sheets than recorded for the Northern Hemisphere. Eastern and central North Island populations of A. hookerianum were characterized by a different subset of haplotypes to populations from the remainder of the country. A similar east-west phylogeographical pattern has been detected in a diverse array of taxa, and has previously been attributed to recurrent vulcanism in the central North Island.

Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae

Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a significant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR amplification primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of five cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL(UAA)-trnF(GAA) intergenic spacer in this group. To these published data we added sequences of the trnS(GCU)-trnG(UUC) intergenic spacer + the trnG(UUC) intron region, the trnS(GGA)-rpS4 intergenic spacer+rpS4 gene, and the rpL16 intron. Both the trnS(GCU)-trnG(UUC) and rpL16 regions are highly variable in angiosperms and the trnS(GGA)-rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the five sampled regions the trnS(GCU)-trnG(UUC) spacer+trnG(UUC) intron region provided the strongest support for the inferred phylogeny.